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Users Manual for KSP Data-Structure-Neutral Codes Implementing Krylov Space Methods

Description: The combination of a Krylov space method and a pre-conditioner is at the heart of most modern numerical codes for the iterative solution of linear systems. This document contains both a users manual and a description of the implementation for the Krylov space methods package KSP included as part of the Portable, Extensible Tools for Scientific computation package (PETSc). PETSc is a large suite of data-structure-neutral libraries for the solution of large-scale problems in scientific computation, in particular on massively parallel computers. The methods in KSP are conjugate gradient method, GMRES, BiCG-Stab, two versions of transpose-free QMR, and others. All of the methods are coded using a common, data-structure-neutral framework and are compatible with the sequential, parallel, and out-of-core solution of linear systems. The codes make no assumptions about the representation of the linear operator; implicitly defined operators (say, calculated using differencing) are fully supported. In addition, unlike all other iterative packages we are aware of, the vector operations are also data-structure neutral. Once certain vector primitives are provided, the same KSP software runs unchanged using any vector storage format. It is not restricted to a few common vector representations. The codes described are actual working codes that run on a large variety of machines including the IBM SP1, Intel DELTA, workstations, networks of workstations, the TMC CM-5, and the CRAY C90. New Krylov space methods may be easily added to the package and used immediately with any application code that has been written using KSP; no changes to the application code are needed.
Date: August 1994
Creator: Gropp, William & Smith, Barry
Partner: UNT Libraries Government Documents Department

Periodized Wavelets

Description: The properties of periodized Daubechies wavelets on [0,1] are detailed and contrasted against their counterparts which form a basis for L{sup 2}(R). Numerical examples illustrate the analytical estimates for convergence and demonstrate by comparison with Fourier spectral methods the superiority of wavelet projection methods for approximations. The analytical solution to inner products of periodized wavelets and their derivatives, which are known as connection coefficients, is presented, and several tabulated values are included.
Date: December 1993
Creator: Schlossnagle, George; Restrepo, Juan Mario & Leaf, G. K.
Partner: UNT Libraries Government Documents Department

Using a Transfer Function to Describe the Load-Balancing Problem

Description: The dynamic load-balancing problem for mesh-connected parallel computers can be clearly described by introducing a function that identifies how much work is to be transmitted between neighboring processors. This function is a solution to an elliptic problem for which a wealth of knowledge exists. The non-uniqueness of the solution to the load-balancing problem is made explicit.
Date: November 1993
Creator: Conley, Andrew J.
Partner: UNT Libraries Government Documents Department

Early Experiences with the IBM SP1 and the High-Performance Switch

Description: The IBM SP1 is IBM`s newest parallel distributed-memory computer. As part of a joint project with IBM, Argonne took delivery of an early system in order to evaluate the software environment and to begin porting programming packages and applications to this machine. This report discusses the results of those efforts once the high-performance switch was installed. An earlier report (ANL/MCS-TM-177) emphasized software usability and the initial ports to the SP1. This report contains performance results and discusses some applications and tools not covered in TM 177.
Date: November 1993
Creator: Gropp, William
Partner: UNT Libraries Government Documents Department

OTTER 3.0 Reference Manual and Guide

Description: OTTER (Organized Techniques for Theorem-proving and Effective Research) is a resolution-style theorem-proving program for first-order logic with equality. OTTER includes the inference rules binary resolution, hyperresolution, UR-resolution, and binary paramodulation. Some of its other abilities and features are conversion from first-order formulas to clauses, forward and back subsumption, factoring, weighting, answer literals, term ordering, forward and back demodulation, evaluable functions and predicates, and Knuth-Bendix completion. OTTER is coded in C, is free, and is portable to many different kinds of computer.
Date: January 1994
Creator: McCune, William W.
Partner: UNT Libraries Government Documents Department

A Parallel Genetic Algorithm for the Set Partitioning Problem

Description: In this dissertation the author reports on his efforts to develop a parallel genetic algorithm and apply it to the solution of set partitioning problem -- a difficult combinatorial optimization problem used by many airlines as a mathematical model for flight crew scheduling. He developed a distributed steady-state genetic algorithm in conjunction with a specialized local search heuristic for solving the set partitioning problem. The genetic algorithm is based on an island model where multiple independent subpopulations each run a steady-state genetic algorithm on their subpopulation and occasionally fit strings migrate between the subpopulations. Tests on forty real-world set partitioning problems were carried out on up to 128 nodes of an IBM SP1 parallel computer. The authors found that performance, as measured by the quality of the solution found and the iteration on which it was found, improved as additional subpopulation found and the iteration on which it was found, improved as additional subpopulations were added to the computation. With larger numbers of subpopulations the genetic algorithm was regularly able to find the optimal solution to problems having up to a few thousand integer variables. In two cases, high-quality integer feasible solutions were found for problems with 36,699 and 43,749 integer variables, respectively. A notable limitation they found was the difficulty solving problems with many constraints.
Date: May 1994
Creator: Levine, David
Partner: UNT Libraries Government Documents Department

Users Guide and Tutorial for PC-GenoGraphics: Version 1

Description: PC-GenoGraphics is a visual database/query facility designed for reasoning with genomic data. Data are represented to reflect variously accurate notions of the location of their sites, etc., along the length of the genome. Sequence data are efficiently stored and queried via a rather versatile language so that entire sequences of organisms will be treatable as they emerge. Other classes of information, such as function descriptions, are stored in a relational form, and joint queries relating these to sequence properties are supported. All queries result in visual responses that indicate locations along the genome. The results of queries can themselves be promoted to be queryable objects against which further queries can be launched.
Date: December 1992
Creator: Hagstrom, Ray; Overbeek, Ross & Price, Morgan
Partner: UNT Libraries Government Documents Department

BlockSolve v1. 1: Scalable Library Software for the Parallel Solution of Sparse Linear Systems

Description: BlockSolve is a software library for solving large, sparse systems of linear equations on massively parallel computers. The matrices must be symmetric, but may have an arbitrary sparsity structure. BlockSolve is a portable package that is compatible with several different message-passing pardigms. This report gives detailed instructions on the use of BlockSolve in applications programs.
Date: March 1993
Creator: Jones, Mark T. & Plassmann, Paul E.
Partner: UNT Libraries Government Documents Department

A Test Implementation of the MPI Draft Message-Passing Standard

Description: Message passing is a common method for programming parallel computers. The lack of a standard has significantly impeded the development of portable software libraries for these machines. Recently, an ad-hoc committee was formed to develop a standard for message-passing software for parallel computers. This group first met in April 1992 at a workshop sponsored in part by the Center for Research on Parallel Computation (CRPC). Four of the attendees at that meeting produced a draft standard, henceforth referred to as the MPI (Message-Passing Interface) draft standard. After review by a larger group, and significant changes in the document, a meeting was held in November to discuss the MPI draft standard. This document is a result of those discussions; it describes a running implementation of in most of the proposed standard, plus additional routines that were suggested by the discussions at the November meeting.
Date: December 1992
Creator: Gropp, William & Lusk, Ewing L.
Partner: UNT Libraries Government Documents Department

Simplified Linear Equation Solvers : Users Manual

Description: The solution of large sparse systems of linear equations is at the heart of many algorithms in scientific computing. The SLES package is a set of easy-to-use yet powerful and extensible routines for solving large sparse linear systems. The design of the package allows new techniques to be used in existing applications without any source code changes in the applications.
Date: February 1993
Creator: Gropp, William & Smith, Barry
Partner: UNT Libraries Government Documents Department

Users manual for the Chameleon Parallel Programming Tools

Description: Message passing is a common method for writing programs for distributed-memory parallel computers. Unfortunately, the lack of a standard for message passing has hampered the construction of portable and efficient parallel programs. In an attempt to remedy this problem, a number of groups have developed their own message-passing systems, each with its own strengths and weaknesses. Chameleon is a second-generation system of this type. Rather than replacing these existing systems, Chameleon is meant to supplement them by providing a uniform way to access many of these systems. Chameleon`s goals are to (a) be very lightweight (low over-head), (b) be highly portable, and (c) help standardize program startup and the use of emerging message-passing operations such as collective operations on subsets of processors. Chameleon also provides a way to port programs written using PICL or Intel NX message passing to other systems, including collections of workstations. Chameleon is tracking the Message-Passing Interface (MPI) draft standard and will provide both an MPI implementation and an MPI transport layer. Chameleon provides support for heterogeneous computing by using p4 and PVM. Chameleon`s support for homogeneous computing includes the portable libraries p4, PICL, and PVM and vendor-specific implementation for Intel NX, IBM EUI (SP-1), and Thinking Machines CMMD (CM-5). Support for Ncube and PVM 3.x is also under development.
Date: June 1993
Creator: Gropp, William & Smith, Barry
Partner: UNT Libraries Government Documents Department

Programming in Fortran M

Description: Fortran M is a small set of extensions to Fortran that supports a modular approach to the construction of sequential and parallel programs. Fortran M programs use channels to plug together processes which may be written in Fortran M or Fortran 77. Processes communicate by sending and receiving messages on channels. Channels and processes can be created dynamically, but programs remain deterministic unless specialized nondeterministic constructs are used. Fortran M programs can execute on a range of sequential, parallel, and networked computers. This report incorporates both a tutorial introduction to Fortran M and a users guide for the Fortran M compiler developed at Argonne National Laboratory. The Fortran M compiler, supporting software, and documentation are made available free of charge by Argonne National Laboratory, but are protected by a copyright which places certain restrictions on how they may be redistributed. See the software for details. The latest version of both the compiler and this manual can be obtained by anonymous ftp from Argonne National Laboratory in the directory pub/fortran-m at info.mcs.anl.gov.
Date: August 1993
Creator: Foster, Ian; Olson, Robert & Tuecke, Steven
Partner: UNT Libraries Government Documents Department

Programming in Fortran M Revision 1

Description: Fortran M is a small set of extensions to Fortran that supports a modular approach to the construction of sequential and parallel programs. Fortran M programs use channels to plug together processes which may be written in Fortran M or Fortran 77. Processes communicate by sending and receiving messages on channels. Channels and processes can be created dynamically, but programs remain deterministic unless specialized nondeterministic constructs are used. Fortran M programs can execute on a range of sequential, parallel, and networked computers. This report incorporates both a tutorial introduction to Fortran M and a users guide for the Fortran M compiler developed at Argonne National Laboratory. The Fortran M compiler, supporting software, and documentation are made available free of charge by Argonne National Laboratory, but are protected by a copyright which places certain restrictions on how they may be redistributed. See the software for details. The latest version of both the compiler and this manual can be obtained by anonymous ftp from Argonne National Laboratory in the directory pub/fortran-m at info.mcs.anl.gov.
Date: October 1993
Creator: Foster, Ian; Olson, Robert & Tuecke, Steven
Partner: UNT Libraries Government Documents Department

Fortran M Language Definition

Description: This document defines the Fortran M extensions to Fortran 77. It updates an earlier definition, dated June 1992, in several minor respects.
Date: August 1993
Creator: Foster, Ian & Chandy, K. Mani
Partner: UNT Libraries Government Documents Department